We are looking at an influenza virus hemaglutinin peptide 306-318 sitting in the groove (magenta) of a human class II MHC molecule (HLA-DR1). We are looking at the face to which the T cell antigen receptor would bind. Most of the 13 amino acid peptide's side chains interact with the lips and floor (yellow) of the groove, but several stick up forming the T cell determinant for this peptide. Compare with the sendai and VSV peptides in MHC class I grooves. Notice that the ends of the longer peptide here protrude out of the ends of the groove.

The peptide uses RasMol's Corey/Pauling/Koltun color scheme: carbon is gray, oxygen is red, and nitrogen is blue. Hydrogens would be white but are not resoved by X-ray crystallography.

This image was constructed from images in a RasMol "movie" script. The atomic coordinate file employed is 1DLH.PDB.

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